Nucleic Acids Biochemistry

4.

Structure and Diversity of Ribonucleic Acid (RNA)

4.1.

Primary Structure of RNA

4.1.1.

RNA Nucleotide Sequence

4.1.1.1.

Base Composition

4.1.1.2.

Sequence Variability

4.1.1.3.

Length Diversity

4.1.2.

4.1.2.1.

Terminal Modifications

4.1.2.2.

Capping Structures

4.1.2.3.

Polyadenylation

4.2.

Secondary Structure

4.2.1.

Base Pairing in RNA

4.2.1.1.

Watson-Crick Pairs

4.2.1.2.

Wobble Base Pairs

4.2.1.3.

Non-Standard Pairs

4.2.2.

Stem-Loop Structures

4.2.2.1.

Hairpin Formation

4.2.2.2.

4.2.2.3.

Stability Factors

4.2.3.

Bulges and Mismatches

4.2.3.1.

Single-Base Bulges

4.2.3.2.

Multi-Base Bulges

4.2.3.3.

4.2.4.

4.2.4.1.

Formation Mechanism

4.2.4.2.

Structural Complexity

4.2.4.3.

Functional Significance

4.2.5.

4.2.5.1.

Loop-Loop Interactions

4.2.5.2.

Tertiary Structure Formation

4.3.

Tertiary Structure

4.3.1.

RNA Folding Principles

4.3.1.1.

Hierarchical Folding

4.3.1.2.

Cooperative Interactions

4.3.1.3.

Kinetic vs Thermodynamic Control

4.3.2.

Stabilizing Interactions

4.3.2.1.

Base Stacking Forces

4.3.2.2.

Metal Ion Coordination

4.3.2.3.

Hydrogen Bonding Networks

4.3.2.4.

Electrostatic Interactions

4.3.3.

Examples of Complex Tertiary Structures

4.3.3.1.

4.3.3.2.

Ribosomal RNA Architecture

4.3.3.3.

Ribozyme Active Sites

4.4.

Major Classes of RNA and Their Functions

4.4.1.

4.4.1.1.

Structure and Features

4.4.1.1.1.

5' Untranslated Region

4.4.1.1.2.

Coding Sequence

4.4.1.1.3.

3' Untranslated Region

4.4.1.1.4.

4.4.1.2.

Function in Protein Coding

4.4.1.2.1.

Genetic Information Transfer

4.4.1.2.2.

Translation Template

4.4.1.2.3.

Regulatory Elements

4.4.1.3.

mRNA Processing

4.4.1.3.1.

4.4.1.3.2.

4.4.1.3.3.

Polyadenylation

4.4.2.

4.4.2.1.

Cloverleaf Structure

4.4.2.1.1.

Secondary Structure Pattern

4.4.2.1.2.

Conserved Regions

4.4.2.1.3.

Variable Regions

4.4.2.2.

L-Shaped Tertiary Structure

4.4.2.2.1.

Three-Dimensional Folding

4.4.2.2.2.

Functional Domains

4.4.2.3.

4.4.2.3.1.

3' CCA Sequence

4.4.2.3.2.

Amino Acid Attachment Site

4.4.2.4.

4.4.2.4.1.

Dihydrouridine Modifications

4.4.2.4.2.

Structural Role

4.4.2.5.

4.4.2.5.1.

Codon Recognition

4.4.2.5.2.

Wobble Position

4.4.2.5.3.

4.4.2.6.

4.4.2.6.1.

Pseudouridine Content

4.4.2.6.2.

Ribosome Binding

4.4.2.7.

Aminoacylation Process

4.4.2.7.1.

Synthetase Recognition

4.4.2.7.2.

ATP Requirement

4.4.2.7.3.

Proofreading Mechanisms

4.4.3.

4.4.3.1.

Structure and Domains

4.4.3.1.1.

Small Subunit rRNA

4.4.3.1.2.

Large Subunit rRNA

4.4.3.1.3.

Conserved Regions

4.4.3.1.4.

Variable Regions

4.4.3.2.

Role in Ribosome Function

4.4.3.2.1.

Peptidyl Transferase Activity

4.4.3.2.2.

Decoding Center Function

4.4.3.2.3.

Structural Framework

4.4.4.

Small Nuclear RNA

4.4.4.1.

U1 snRNA Function

4.4.4.2.

U2 snRNA Function

4.4.4.3.

U4/U6 snRNA Complex

4.4.4.4.

U5 snRNA Function

4.4.4.5.

Role in Splicing

4.4.4.5.1.

Spliceosome Assembly

4.4.4.5.2.

Splice Site Recognition

4.4.4.5.3.

Catalytic Function

4.4.5.

4.4.5.1.

Biogenesis Pathway

4.4.5.1.1.

Primary Transcript Processing

4.4.5.1.2.

Precursor miRNA Formation

4.4.5.1.3.

Mature miRNA Generation

4.4.5.2.

Role in Gene Regulation

4.4.5.2.1.

Target mRNA Recognition

4.4.5.2.2.

Translation Repression

4.4.5.2.3.

mRNA Degradation

4.4.6.

Small Interfering RNA

4.4.6.1.

Biogenesis Pathway

4.4.6.1.1.

Double-Strand RNA Processing

4.4.6.1.2.

4.4.6.1.3.

4.4.6.2.

Role in RNA Interference

4.4.6.2.1.

Target Recognition

4.4.6.2.2.

4.4.6.2.3.

Chromatin Modification

4.4.7.

Long Non-coding RNA

4.4.7.1.

Types and Classifications

4.4.7.1.1.

Intergenic lncRNA

4.4.7.1.2.

Antisense lncRNA

4.4.7.1.3.

Intronic lncRNA

4.4.7.2.

4.4.7.2.1.

Transcriptional Regulation

4.4.7.2.2.

Chromatin Modification

4.4.7.2.3.

Post-Transcriptional Control

4.4.7.2.4.

Protein Scaffolding

4.4.8.

Other RNA Classes

4.4.8.1.

Small Nucleolar RNA

4.4.8.2.

PIWI-Interacting RNA

4.4.8.3.

4.4.8.4.

4.5.

Catalytic RNA: Ribozymes

4.5.1.

Types of Ribozymes

4.5.1.1.

Group I Introns

4.5.1.2.

Group II Introns

4.5.1.3.

4.5.1.4.

Hammerhead Ribozymes

4.5.1.5.

Hairpin Ribozymes

4.5.1.6.

Peptidyl Transferase Center

4.5.2.

Mechanisms of Catalysis

4.5.2.1.

Metal Ion Catalysis

4.5.2.2.

Acid-Base Catalysis

4.5.2.3.

Electrostatic Stabilization

4.5.2.4.

Conformational Changes

4.5.3.

Biological Roles

4.5.3.1.

4.5.3.2.

Protein Synthesis

4.5.3.3.

Gene Regulation

4.5.3.4.

Evolutionary Significance

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5. Nucleic Acid Metabolism: Biosynthesis